A5082317014- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Pancreatic and Hepatic Oncology Research
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- T-cell and B-cell Immunology
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- Genomics and Rare Diseases
- Immune cells in cancer
- EEG and Brain-Computer Interfaces
- Renal and related cancers
- Diabetes and associated disorders
- RNA modifications and cancer
- Neural dynamics and brain function
- Genomics and Phylogenetic Studies
- Blind Source Separation Techniques
- Extracellular vesicles in disease
- Histone Deacetylase Inhibitors Research
- Digital Imaging for Blood Diseases
- Genetic Associations and Epidemiology
- Cytokine Signaling Pathways and Interactions
Western University
2020-2025
Children’s Health Research Institute
2020-2024
Ontario Institute for Cancer Research
2020-2024
Lawson Health Research Institute
2020-2024
London Health Sciences Centre
2020
Hospital for Sick Children
2018-2019
SickKids Foundation
2018
Yale University
2015-2017
Broad Institute
2016-2017
BC Cancer Agency
2010-2011
Abstract Background Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral particular has proven to be a powerful tool amenable applications. However, it cannot directly applied due time and memory limitations. To address this issue, we modified spectral by adding an information preserving sampling procedure applying post-processing stage. We call entire algorithm SamSPECTRAL. Results tested our on flow...
Abstract The immune response in humans is usually assessed using immunogenicity assays to provide biomarkers as correlates of protection (CoP). Flow cytometry the assay choice measure intracellular cytokine staining (ICS) cell‐mediated (CMI) biomarkers. For CMI analysis, integrated mean fluorescence intensity (iMFI) was introduced a metric represent total functional CoP. iMFI computed by multiplying relative frequency (percent positive) cells expressing particular with MFI that population,...
Mucosa-associated invariant T (MAIT) cells are unconventional, innate-like lymphocytes that recognize vitamin B metabolites of microbial origin among other antigens displayed by the monomorphic molecule MHC class I-related protein 1 (MR1). Abundant in human tissues, reactive to local inflammatory cues, and endowed with immunomodulatory cytolytic functions, MAIT likely play key roles malignancies. They accumulate various tumor microenvironments (TMEs) where they often lose some their...
Abstract B cells have been shown to be phagocytic under some circumstances. However, the capacity of different cell subsets and how this is linked Antigen (Ag) presentation or other functions has not characterized. To address this, we developed 2 µm Ag conjugated bead targets that target pathways including BCR, scavenger, Fc, complement receptors study potential by which phagocytose both cognate non-cognate Ags. We found while follicular B2 (Fo B), marginal zone, B1 are highly BCR-engaging...
CReSCENT: CanceR Single Cell ExpressioN Toolkit (https://crescent.cloud), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data tumour specimens are readily generated, subsequent requires high-performance computing infrastructure user expertise to build pipelines tailor interpretation cancer biology. CReSCENT uses public sets preconfigured that accessible...
Motivation The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to collect present related TME data in an easily accessible format. Results We therefore built database, created the R package TMExplorer facilitate investigation of TME. provides interface...
Epstein-Barr virus (EBV) causes lifelong infection in over 90% of the world’s population. EBV leads to several types B cell and epithelial cancers due viral reprogramming host-cell growth gene expression. is associated with 10% stomach/gastric adenocarcinomas (EBVaGCs), which have distinct molecular, pathological, immunological characteristics compared EBV-negative gastric (EBVnGCs). Publicly available datasets, such as The Cancer Genome Atlas (TCGA), contain comprehensive transcriptomic,...
Using robust, integrated analysis of multiple genomic datasets, we show that genes depleted for non-synonymous de novo mutations form a subnetwork 72 members under strong selective constraint. We further this is preferentially expressed in the early development human hippocampus and enriched mutated neurological Mendelian disorders. thus conclude carefully orchestrated developmental processes are constraint brain development, perturbations caused by mutation have adverse outcomes subject to...
Abstract International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets open chromatin regions publicly available. While these are extremely useful for studying mechanisms gene regulation in disease cell development, they only identify individual samples. A uniform comparison accessibility the same regulatory sites across multiple samples is necessary to correlate expression target genes matched types....
Flow cytometry is a widely used analytical technique for examining microscopic particles, such as cells. The Cytometry Standard (FCS) was developed in 1984 storing flow data and it supported by all instrument third party software vendors. However, FCS does not capture the full scope of (FCM)-related metadata, standards have recently been to address this shortcoming.The Data Standards Task Force (DSTF) International Society Advancement (ISAC) has several complement raw encoded files. Efforts...
Reactivation of the multi-subunit ribonucleoprotein telomerase is primary telomere maintenance mechanism in cancer, but it rate-limited by enzymatic component, reverse transcriptase (TERT). While regulatory nature, TERT alternative splice variant/isoform regulation and functions are not fully elucidated further complicated their highly diverse expression nature. Our objective was to characterize isoform across 7887 neoplastic 2099 normal tissue samples using The Cancer Genome Atlas (TCGA)...
Single-cell RNA sequencing (scRNA-seq) clustering and labelling methods are used to determine precise cellular composition of tissue samples. Automated rely on either unsupervised, cluster-based approaches or supervised, cell-based identify cell types. The high complexity cancer poses a unique challenge, as tumor microenvironments often composed diverse subpopulations with functional effects that may lead disease progression, metastasis treatment resistance. Here, we assess 17 9 scRNA-seq...
EEG signal is one of the oldest measures brain activity that has been used vastly for clinical diagnoses and biomedical researches. However, signals are highly contaminated with various artifacts, both from subject equipment interferences. Among these kinds ocular noise most important one. Since many applications such as BCI require online real-time processing signal, it ideal if removal artifacts performed in an fashion. Recently, some methods artifact removing have proposed. One ARMAX...
Tumors are complex biological entities that comprise cell types of different origins, with mutational profiles and patterns transcriptional dysregulation. The exploration data related to cancer biology requires careful analytical methods reflect the heterogeneity populations in samples. Single-cell techniques now able capture individual cells. However, complexity RNA-seq data, especially samples, makes it challenging cluster single-cell into groups underlying types. We have developed a...
ABSTRACT International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets open chromatin regions publicly available. While these are extremely useful for studying mechanisms gene regulation in disease cell development, they only identify individual samples. A uniform comparison accessibility the same regulatory sites across multiple samples is necessary to correlate expression target genes matched types....
Genome-wide association studies in autoimmune and inflammatory diseases (AID) have uncovered hundreds of loci mediating risk 1,2 . These associations are preferentially located non-coding DNA regions 3,4 particular to tissue-specific Dnase I hypersensitivity sites (DHS) 5,6 Whilst these analyses clearly demonstrate the overall enrichment disease alleles on gene regulatory regions, they not designed identify individual or genes under their control, thus uncover specific molecular events...
Due to the large volume required for medical images transmission and archiving purposes, compression of is known as one main concepts image processing. Lossless methods have drawback a low ratio. In contrast, lossy higher ratio suffer from lower quality reconstructed in receiver. Recently, some selective been proposed which divided into two separate regions: Region Interest (ROI), should be compressed lossless manner, Background (ROB), manner with quality. this research, we introduce new...
ABSTRACT Autoimmune and inflammatory diseases are a group of > 80 complex caused by loss immune tolerance for self-antigens. The biological mechanisms autoimmune largely unknown, preventing the development effective treatment options. Integrative analysis genome-wide association studies chromatin accessibility data has shown that risk variants enriched in open regions cells, supporting their role gene regulation. However, we still lack systematic unbiased identification transcription...
Abstract Introduction: Over 90% of PDAC patients harbor an activating KRAS mutation, the most common form being KRASG12D. However, additional genetic mutations and environmental events, including chronic or hereditary pancreatitis, are needed for to lead PDAC. Our laboratory showed Activating Transcription Factor 3 (ATF3) was required repressing genes that stabilize mature acinar cell phenotype KRASG12D-driven progression advanced PanIN lesions. ATF3 contributes gene activation repression...
The fundamental biology of pancreatic ductal adenocarcinoma has been greatly impacted by the characterization genetically engineered mouse models that allow temporal and spatial activation oncogenic KRAS (KRAS
Enhancer of Zeste Homologue 2 (EZH2) is part the Polycomb Repressor Complex 2, which promotes trimethylation lysine 27 on histone 3 (H3K27me3) and genes repression. EZH2 overexpressed in many cancers studies mice attributed both pro-oncogenic tumor suppressive functions to pancreatic ductal adenocarcinoma (PDAC). deletion enhances de novo KRAS-driven neoplasia following injury, while increased expression PDAC patients correlated poor prognosis, suggesting a context-dependant effect for...
ABSTRACT CReSCENT CanceR Single Cell ExpressioN Toolkit ( https://crescent.cloud ), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data tumour specimens are readily generated, subsequent requires high-performance computing infrastructure user expertise to build pipelines tailor interpretation cancer biology. uses public sets preconfigured that accessible...